I just want to know if there is a way to duplicate an eclipse workspace including the projects inside.
EDIT : Copying files doesn't work for me, I'm looking for an automated process or a plugin.
I am not aware of any automated solution. The worskpace itself (in the .metadata directory) contains absolute paths and that's the reason why you cannot simply copy it.
I always duplicate workspace by creating a new one. It may be more complicated, but it always works. I have all the eclipse-project files (.settings directory) in a versioning system which makes creating brand new workspace relatively simple. After creating empty workspace, I just use Import -> Existing Projects into Workspace.